Hi Bill,
Thanks a lot for answering my E-mail !!!. Though, as you can see from
the title of this E-mail the problem was resolved. As I suspected, the
problem emerged due to the trajectory post-processing.
I thank you nevertheless for all your help !!!
Best wishes,
Arik
On 8/6/2010 4:50 PM, Bill Ross wrote:
>> When visualizing an equilibration trajectory (for 2ns, with 10000
>> snapshots, taken every 100 steps, each step is 2fs), the trajectory is
>> well behaving though after a while it collapses to a small ball like,
>> appearing in different places every couple of steps(like in different
>> unit cells). This problem seems to be a post-processing error as the
>> potential and kinetic energy a long the trajectory seems just fine. i.e
>> as they should be with no abnormal fluctuations.
>> It should be mentioned, that this problem appears in both occasions when
>> processing the mdcrd file to a truncated mdcrd or a truncated binpos
>> file using ptraj.
> Can you show your ptraj script? Can you view the whole trajectory
> if it isn't massaged by ptraj? If you are stripping any atoms, are
> you sure you are using a correct prmtop? Is it all from a single mdcrd?
> What program are you using to visualize?
>
> Bill
>
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Received on Fri Aug 06 2010 - 18:30:03 PDT
